Single-Molecule Localization Microscopy  •  Software Benchmarking

The Challenge 2013 is turned to an online permanent challenge

The Grand Challenge Localization Microscopy was organized as Workshop in the conference IEEE International Symposium on Biomedical Imaging. Nearly 30 software have been run, mostly by the authors of the software, thus constituting the first world-wide effort in benchmarking the localization software in a comprehensive review. The results are now published.

The 2013 ISBI challenge is now re-open as a online permanent challenge and a new SMLM challenge will be held in 2016.

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Methods

1. Simulator

2. Sample Factory

3. Fluorophore Factory

4. Image Formation Model (PSF)

5. Noise Model and Digitalization

6. Metrics of asssessment

7. Format

8. Rendering

1. Simulator

simulation

2. Sample Factory

factory

3. Fluorophore Factory

factory

4. Image Formation Model (PSF)

psf

5. Noise Model and Digitalization

noise

6. Metrics of asssement

7. Format

Towards standardization of the file format Interactive Creation of the XML Description File

The results of the localization are given in a delimiter-separated values text file. Every localization position of each frame is stored as row in this file. The description file is a XML that helps to decode the localization file format and it gives the spatial reference allowing comparaison.

Required information for each row

  • Mandatory - Frame number starting from 1
  • Mandatory - Position in X axis (in nm)
  • Mandatory - Position in Y axis (in nm)
  • Optional - Position in Z axis (in nm)
  • Optional - Measured intensity
  • Optional - Confidence in the measurement (%)
Description XML File
Organization
Separator of columns Required
Unit for the XY position default in nm
Row of the first localization
 
Column index • Important note: column index starts at 0
Column of the frame Required
Column for the X position Required
Column for the Y position Required
Column for the Z position Optional
Column for the intensity Optional
Column for the confidence (%) Optional
 
Shift of the origin • Check the figure
X shift default value: 0
Y shift default value: 0
Z shift default value: 0
Unit shift default in pixel
 
Shift in the numbering of the frames • Convention: 1 for the first frame
Frame shift default value: 0

Predefined settings

8. Rendering

PALM-siever • Visualization for Single-Molecule Localization Microscopy

palm-siever

For this challenge, we use PALM-siever as tool to render the reconstruction image from the localization results. PALM-siever is hosted by Google Project.

The PALM-siever platform covers both visualization and analysis of single-molecule localization microscopy data. Built on MATLAB, it enables data to be modified and displayed interactively.

Features

  • histogram, smoothed histogram, scatter, delaunay, color-coded 3D
  • smart import of tabular data
  • interactive slicing with any variable
  • plugins
  • palm-siever

© 2017 Biomedical Imaging Group, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
Last update: 31 Mar 2017